Scott and playing partner Rickie Fowler marked their balls on the 12th fairway after a severe storm warning suspended play with Scott holding a one-shot lead.
When Scott returned, his iron shot from the fairway nearly holed out for an albatross and he made the 1-foot eagle putt.
Scott was 4 under in his seven holes after the weather suspension. Fowler finished second with 68.
Making his first appearance back in Australia since his April win at Augusta, Scott finished with 14-under 270 at Royal Pines.
Scott joins Greg Norman, Craig Parry, Peter Lonard, Robert Allenby and Peter Senior as the only Australian golfers to add the Joe Kirkwood Cup for winning the Australian PGA to the Australian Open and Australian Masters titles in their careers. Those three tournaments are considered the Australian majors.
“I came out and knew I had to do something great to win this,” Scott said. “It’s been an incredible year since April, and so great to come home. I’ve had a great week.”
EUROPEAN TOUR: In Antalaya, Turkey, Victor Dubuisson won the inaugural Turkish Airlines Open for his first European Tour title, beating Jamie Donaldson by two strokes.
Dubuisson closed with 3-under 69 to finish at 24-under 264. Donaldson had a hole-in-one at the 16th in 63.
Tiger Woods and Justin Rose tied for third, four shots back. Woods, who won’t play again until the World Challenge on Dec. 5 in Thousand Oaks, Calif., shot 67. Rose had 65.
LPGA TOUR: In Shima, Japan, Teresa Lu won the Mizuno Classic, birdieing the last two holes and six of the final eight for a two-stroke victory.
The 25-year-old Lu, a regular on the Japan LPGA Tour after giving up her LPGA Tour membership in 2010, shot 8-under 64 in windy, wet conditions at Kintetsu Kashikojima. She finished at 14-under 202 and earned her first professional title.
Chella Choi, tied with Lu with two holes to play, had 66 to finish second.
American Stacy Lewis, the 2012 winner, tied for eighth at 7 under after 70. Brittany Lincicome, a stroke behind second-round leaders Higa, Ichinose and Oyama entering the day, had 77 to tie for 29th at 2 under.